Problem in running optimizemetrics.

ok..now its working....thank you...

Hi,


I reckon the pharma-frag.xml configuration file is not compatible with the optimizemetrics application. Which version of jchem are you using?


Does the 4th line of the XML configuration file begin with the "PharmacophoreFingerprintConfiguration" keyword or not?


Regards,


Miklos

Hi,


i am using JChem 3.2.3 version .


this is the 4 th line of the XML file" <PharmacophoreConfiguration Version ="0.3" schemaLocation="pharmacophores.xsd">"





attaching the XML also..

This is an old file that should not be in that JChem distribution. Apologies, we will correct the file in the next release of JChem.





There should be "PharmacophoreFingerprintConfiguration" instead of "PharmacophoreConfiguration", will you please correct it in your XML file? The rest of the file is just fine, I hope this solves the problem.





Regards,


Miklos

hi,


i have corrected the XML and tried, but i am getting the following message:





OptimizeMetrics - Molecular Descriptor Dissimilarity Metrics Optimizer 3.2.3,


(C) 2002-2007 ChemAxon Ltd.





No valid license key has been found for OptimizeMetrics.


The maximal number of calls (103) without a license key has been reached.


Please contact sales _at_ chemaxon.com to obtain a license key.


Students and academic researchers can obtain license keys


for free through our Academic Package, for more information


please visit: http://www.chemaxon.com.


chemaxon.marvin.modules.LicenseException: No valid license key has been found fo


r OptimizeMetrics.


The maximal number of calls (103) without a license key has been reached.


Please contact sales _at_ chemaxon.com to obtain a license key.


Students and academic researchers can obtain license keys


for free through our Academic Package, for more information


please visit: http://www.chemaxon.com.


at chemaxon.marvin.modules.LicenseManager$CallCounter.call(LicenseManage


r.java:145)


at chemaxon.marvin.modules.LicenseManager.call(LicenseManager.java:705)


at chemaxon.descriptors.OptimizeMetrics.main(OptimizeMetrics.java:225)





can u tell me whats the problem??

I reckon you need to ask sales for the license keys. Though you should have received them after the registration procedure was completed. Did you get them at all?


Did you manage to install them? Still having problems?


Perhaps this link may provide some help: http://www.chemaxon.com/jchem/doc/user/Licenses.html





Miklos

i have the academid package and license key...


Thanks for your response..





now my problem is that i have tried to run optimizer with many parameters





for e.g OptimizeMetrics input\nci300.smiles input\ace-1-4.smiles input\ace-5-8.smiles -e 3 -H -v -f Enrichment -k CF -c input\cfp.xml -o opt-CF.xml -M Tanimotot Tanimoto -M Tanimotoa Tanimoto -a -M Euclideant Euclidean -M Euclideann Euclidean -n -M Euclideana Euclidean -a -k PF -o output\opt-PF.xml -c input\pharma-frag.xml -M Tanimotot Tanimoto -M Tanimotos Tanimoto -s -M Tanimotoa Tanimoto -a -M Tanimotosa Tanimoto -s -a -M Euclideant Euclidean -M Euclideann Euclidean -n -M Euclideanwn Euclidean -w -n -M Euclideana Euclidean -a -M Euclideanwa Euclidean -w -a -M Euclideanan Euclidean -a -n -M Euclideanwan Euclidean -w -a -n





but showing error that :


Error: Too many parameters. You are probably not using quotes for parameters


that contain more words.





can u tell me why..


we can use these many metrics options(parameters for metrics) in this program right???

Hi,





my query was :


OptimizeMetrics input\nci300.smiles input\ace-1-4.smiles input\ace-5-8.smiles -e 3 -H -v -f Enrichment -k CF -c input\cfp.xml -o output\opt-CF.xml-M Tanimotot Tanimoto -M Tanimotoa Tanimoto -a -M Euclideant Euclidean -M Euclideann Euclidean -n -M Euclideana Euclidean -a





and it runs successfully and got the XML file.Then i did the Hitstatistics program,





hitstatistics input\nci700.smiles input\ace-9-16.smiles input\ace-5


-8.smiles -o output\hitstatCF.sdf -e 3 -b -k CF -c output\opt-CF.xml





this also run successfully ..





see the attachment.


my question is that in that result file , all the metrics have the same result,


CF Euclidean 1 0.5 -1 10 8 700 700 700, 0, 0, 0, 0, 0, 0, 0





here target set is 700, "Target Hits: number of hits from the random target set, the smaller the better "





Then what will came to know from this output??/

This earlier post may help: http://www.chemaxon.com/forum/viewpost10072.html#10072





Miklos